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Crystal structure of S. aureus fabi in complex with NADP and 5-hexyl-2-(2-METHYLPHENOXY)PHENOL

Analyse Crystal structure of S. aureus fabi in complex with NADP and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4BNM
Type: protein
Length: 2,037 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Enoyl-[acyl-carrier-protein] reductase [NADPH]
EC: 1.3.1.10
UniProt: Q7A6D8
Ligands: TCU, NAP, GLU
Pockets: 20 · best druggability 0.89

Structure

x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, D, H	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	254	50% helix, 15% strand	Q7A6D8
B, C, E, F, G	Enoyl-[acyl-carrier-protein] reductase [NADPH] (EC 1.3.1.10)	protein	255	50% helix, 15% strand	Q7A6D8

Ligands and binding sites

TCU · 5-hexyl-2-(2-methylphenoxy)phenol · ligand · 8 copies · chains A, B, C, D, E, F, G, H
NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 8 copies · chains A, B, C, D, E, F, G, H
GLU · Glutamic acid · ligand · 5 copies · chains B, C, A, E, F, G

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

20 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1178	0.89	0.91	104	TCU, NAP
2	1105	0.85	0.86	65	empty
3	1143	0.85	0.86	68	empty
4	541	0.83	0.89	51	NAP, TCU
5	531	0.83	0.89	51	NAP, TCU

Interfaces

15 interfaces between chains.

C–D · 1814 Å² buried · 46 hydrogen bonds · protein-protein
G–H · 1799 Å² buried · 42 hydrogen bonds · protein-protein
E–F · 1785 Å² buried · 41 hydrogen bonds · protein-protein
A–B · 1780 Å² buried · 44 hydrogen bonds · protein-protein
B–C · 1408 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

4BNM · Crystal structure of S. aureus FabI in complex with NADP and 5-hexyl… · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt Q7A6D8
Elsewhere: RCSB PDB 4BNM · PDBe 4BNM · UniProt Q7A6D8

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